dbSNP rs11693697: ENSG00000304533:n.698+584T>C (chr2-102299202-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000804381.1(ENSG00000304533):n.698+584T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,186 control chromosomes in the GnomAD database, including 1,646 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.13 ( 1646 hom., cov: 32)

Consequence

ENSG00000304533
ENST00000804381.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.258

Publications

17 publications found

Variant links:

Genes affected

ENSG00000304533 (HGNC:):

ENSG00000304533 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304533	ENST00000804381.1 link	n.698+584T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19233

AN:

152068

Hom.:

1646

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0338

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.116

Gnomad ASJ

AF:

0.126

Gnomad EAS

AF:

0.00192

Gnomad SAS

AF:

0.0680

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.133

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.126

AC:

19225

AN:

152186

Hom.:

1646

Cov.:

AF XY:

0.125

AC XY:

9291

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.0337

AC:

1400

AN:

41560

American (AMR)

AF:

0.115

AC:

1766

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.126

AC:

438

AN:

3472

East Asian (EAS)

AF:

0.00193

AC:

AN:

5188

South Asian (SAS)

AF:

0.0674

AC:

325

AN:

4820

European-Finnish (FIN)

AF:

0.200

AC:

2111

AN:

10574

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.187

AC:

12679

AN:

67960

Other (OTH)

AF:

0.132

AC:

279

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

816

1632

2447

3263

4079

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

214

428

642

856

1070

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.158

Hom.:

4401

Bravo

AF:

0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.16

(source)

DANN

Benign

0.45

PhyloP100

-0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over